6TH IFAC CONFERENCE ON FOUNDATIONS OF SYSTEMS BIOLOGY IN ENGINEERING FOSBE 2016
Universität Magdeburg
Magdeburg, Germany
October 9-12, 2016
  
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Last updated on September 29, 2016. This conference program is tentative and subject to change

Technical Program for Monday October 10, 2016

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MoOP Opening, Nave Add to My Program 
Opening  
 
 
MoPMP Plenary Session, Nave Add to My Program 
Guy-Bart Stan  
 
 
08:45-09:30, Paper MoPMP.1 Add to My Program
Control Engineering Meets Synthetic Biology: Shared Resources and Feedback Considerations for Better Engineering of Bacterial Cells
Stan, Guy-Bart (Imperial Coll)
 
MoKMP Keynote Session, Nave Add to My Program 
Robert S. Parker  
 
 
09:30-10:00, Paper MoKMP.1 Add to My Program
A "Virtual Patient" Cohort and Mathematical Model of Glucose Dynamics in Critical Care
Knab, Timothy D. (Univ. of Pittsburgh), Clermont, Gilles (Univ. of Pittsburgh), Parker, Robert S. (Univ. of Pittsburgh)
 
MoCMP Coffee, Nave Add to My Program 
Coffee Break MM  
 
 
MoM1 Regular Session, Nave Add to My Program 
Synthetic Biology  
 
 
10:30-10:50, Paper MoM1.1 Add to My Program
Dynamic Network Analysis Combined with Protein-Protein Interaction Knowledge Identified Short Feedback and Feed-Forward Circuits in Genetic Networks
Bar, Nadav S. (Norwegian Univ. of Science and Tech), Jayavelu, Naresh D. (Univ. of Turku and Ĺbo Akademi Univ)
 
10:50-11:10, Paper MoM1.2 Add to My Program
Control of Gene Expression for the Study of Neurodegenerative Disorders: A Proof-Of-Principle Experimental Study
Perrino, Giansimone (Univ. of Naples Federico II), Wilson, Cathal (TIGEM), Santorelli, Marco (TIGEM), di Bernardo, Diego (TIGEM, Univ. of Naples Federico II)
 
11:10-11:30, Paper MoM1.3 Add to My Program
A Multiobjective Optimization Approach to the Forward and Reverse Design of Biological Oscillators
Otero-Muras, Irene (IIM-CSIC), Banga, Julio R. (IIM-CSIC (Spanish Council for Scientific Res)
 
11:30-11:50, Paper MoM1.4 Add to My Program
From a Discrete to Continuous Actuation for Improved Real-Time Control of Gene Expression in Mammalian Cells
Postiglione, Lorena (TIGEM, Univ. of Naples Federico II), Santorelli, Marco (TIGEM, Univ. of Naples Federico II), Tumaini, Barbara (TIGEM, Univ. of Naples Federico II), di Bernardo, Diego (TIGEM, Univ. of Naples Federico II)
 
11:50-12:10, Paper MoM1.5 Add to My Program
Bringing the Parts Together: Steps towards an In-Silico Protocell
Schneider, Eugenia (Max-Planck-Inst. for Dynamics of Complex Tech. Systems), Schweizer, Jakob (Max Planck Inst. for Dynamics of Complex Tech. Systems), Mangold, Michael (Max Planck Inst. for Dynamics of Complex Tech. Systems)
 
MoM2 Regular Session, Gallery Add to My Program 
Modelling – Health  
 
 
10:30-10:50, Paper MoM2.1 Add to My Program
A Simplified 2D Heart Model of the Wolff-Parkinson-White Syndrome
Zeile, Clemens (Univ. of Magdeburg), Scholz, Eberhard (Univ. Hospital Heidelberg), Sager, Sebastian (Otto-Von-Guericke Univ. Magdeburg)
 
10:50-11:10, Paper MoM2.2 Add to My Program
Spatiotemporal Metabolic Modeling of a Chronic Wound Biofilm Consortium
Phalak, Poonam (Univ. of Massachusetts), Chen, Jin (Univ. of Massachusetts), Carlson, Ross P. (Montana State Univ), Henson, Michael A. (Univ. of Massachusetts)
 
11:10-11:30, Paper MoM2.3 Add to My Program
Coupling Cellular Phenotype and Mechanics to Understand Extracellular Matrix Formation and Homeostasis in Osteoarthritis
Sunkara, Vikram (Freie Univ. Berlin, ZIB), von Kleist, Max (Freie Univ. Berlin)
 
11:30-11:50, Paper MoM2.4 Add to My Program
Parameter Estimation for Leukocyte Dynamics after Chemotherapy
Rinke, Kristine (Otto-Von-Guericke-Univ. Magdeburg), Jost, Felix (Otto-Von-Guericke-Univ. Magdeburg), Findeisen, Rolf (Otto-Von-Guericke-Univ. Magdeburg), Fischer, Thomas (Univ. Hospital Magdeburg), Bartsch, Rainer (Univ. Hospital Magdeburg), Schalk, Enrico (Univ. Hospital Magdeburg), Sager, Sebastian (Otto-Von-Guericke-Univ. Magdeburg)
 
11:50-12:10, Paper MoM2.5 Add to My Program
Invariant Based Control of Induction and Maintenance Phases for Anesthesia
Fiacchini, Mirko (GIPSA-Lab, CNRS), Queinnec, Isabelle (LAAS-CNRS), Tarbouriech, Sophie (LAAS-CNRS), Mazerolles, Michel (CHU Toulouse)
 
MoPP Poster Session, Nave Add to My Program 
Lunch + Poster Session I  
 
 
12:10-14:10, Paper MoPP.1 Add to My Program
Normalization of Western Blot Data Affects the Statistics of Estimators
Thomaseth, Caterina (Univ. of Stuttgart), Radde, Nicole (Univ. of Stuttgart)
 
12:10-14:10, Paper MoPP.2 Add to My Program
New Concepts for Evaluating the Performance of Computational Methods
Kreutz, Clemens (Albert-Ludwigs-Univ. Freiburg)
 
12:10-14:10, Paper MoPP.3 Add to My Program
A Constrained NMF Approach to Analyze Quantitative Metagenomic Data
Raguideau, Sébastien (MaIAGE, INRA, Univ. Paris-Saclay), Laroche, Béatrice (MaIAGE, INRA, Univ. Paris-Saclay), Leclerc, Marion (Micalis, INRA, Univ. Paris-Saclay), Plancade, Sandra (MaIAGE, INRA, Univ. Paris-Saclay)
 
12:10-14:10, Paper MoPP.4 Add to My Program
Parameter Identification in Synthetic Biological Circuits Using Multi-Objective Optimization
Boada, Yadira (Univ. Pol. De Valencia), Vignoni, Alejandro (Max Planck Inst. of Molecular Cell Biology and Genetics), Reynoso-Meza, Gilberto (Pontificia Univ. Católica De Paraná), Picó, Jesús (Univ. Pol. De Valencia)
 
12:10-14:10, Paper MoPP.5 Add to My Program
A Parallel Modelling Algorithm for Simulating Calcium Release in Cells
Stoddard, Jeremy G. (Univ. of Newcastle), Welsh, James S. (Univ. of Newcastle), Laver, Derek R. (Univ. of Newcastle)
 
12:10-14:10, Paper MoPP.6 Add to My Program
Preconditioned Metropolis Sampling As a Strategy to Improve Efficiency in Posterior Exploration
Engblom, Stefan (Uppsala Univ), Sunkara, Vikram (FU Berlin, ZIB)
 
12:10-14:10, Paper MoPP.7 Add to My Program
Integrating Classifiers across Datasets Improves Consistency of Biomarker Predictions for Sepsis
Saraiva, Joăo Pedro (Hans Knöll Inst. Centre for Sepsis Control and Care), Oswald, Marcus (Hans Knöll Inst. Centre for Sepsis Control and Care), Biering, Antje (Hans Knöll Inst. Centre for Sepsis Control and Care), Assman, Cora (Septomics Res. Centre, Jena Univ. Hospital), Klassert, Tilman (Septomics Res. Centre, Jena Univ. Hospital), Blaess, Markus (Centre for Sepsis Control and Care, Jena Univ. Hospital), Czakai, Kristin (Univ. Hospital Würzburg), Claus, Ralf (Centre for Sepsis Control and Care, Jena Univ. Hospital), Löffler, Jürgen (Univ. Hospital Würzburg), Slevogt, Hortense (Septomics Res. Center, Jena Univ. Hospital), König, Rainer (Hans Knöll Inst. Centre for Sepsis Control and Care)
 
12:10-14:10, Paper MoPP.8 Add to My Program
A Curvilinear Model Approach: Actin Cortex Clustering Due to ATP-Induced Myosin Pulls
Wölfer, Christian (Max Planck Inst. for Dynamics of Complex Tech. Systems), Vogel, Sven K. (Max Planck Inst. of Biochemistry), Mangold, Michael (Max Planck Inst. for Dynamics of Complex Tech. Systems)
 
12:10-14:10, Paper MoPP.9 Add to My Program
Optimising Time-Series Experimental Design for Modelling of Circadian Rhythms: The Value of Transient Data
Mombaerts, Laurent (Univ. Du Luxembourg), Mauroy, Alexandre (Univ. of Luxembourg), Goncalves, Jorge M. (Univ. of Luxembourg)
 
12:10-14:10, Paper MoPP.10 Add to My Program
Validation Methods for Population Models of Gene Expression Dynamics
González-Vargas, Andrés M. (Univ. Autónoma De Occidente), Cinquemani, Eugenio (INRIA Grenoble - Rhône-Alpes), Ferrari-Trecate, Giancarlo (Univ. Degli Studi Di Pavia)
 
12:10-14:10, Paper MoPP.11 Add to My Program
Using Optimal Control to Understand Complex Metabolic Pathways
Tsiantis, Nikolaos (IIM-CSIC (Spanish Council for Scientific Res), Banga, Julio R. (IIM-CSIC (Spanish Council for Scientific Res)
 
12:10-14:10, Paper MoPP.12 Add to My Program
Parameter Estimation in Models of Biological Oscillators: Pitfalls and Solutions
Pitt, Jake Alan (BioProcess Engineering Group, IIM-CSIC, 36208 Vigo (Spain)), Banga, Julio R. (IIM-CSIC (Spanish Council for Scientific Res)
 
12:10-14:10, Paper MoPP.13 Add to My Program
Modeling, Optimization and Control of Biological Systems with AMIGO2
Balsa-Canto, Eva (CSIC), Henriques, David (IIM-CSIC), Gabor, Attila (Mta Sztaki), Banga, Julio R. (IIM-CSIC (Spanish Council for Scientific Res)
 
12:10-14:10, Paper MoPP.14 Add to My Program
Identifiability Analysis of Dynamic Models in Systems Biology: A Combined Structural, Practical, and Graphical Approach
Fernández Villaverde, Alejandro (Univ. De Vigo), Gabor, Attila (Mta Sztaki), Banga, Julio R. (IIM-CSIC (Spanish Council for Scientific Res)
 
12:10-14:10, Paper MoPP.15 Add to My Program
Letting Data Choose the 13C Flux Model: On How to Do It and the Consequences of (not) Doing It
Theorell, Axel (Forschungszentrum Jülich), Leweke, Samuel (IBG-1: Biotechnology, Forschungszentrum Jülich GmbH), Wiechert, Wolfgang (IBG-1: Biotechnology, Forschungszentrum Jülich GmbH), Rocco, Andrea (Faculty of Health and Medical Sciences, Univ. of Surrey), McFadden, Johnjoe (Faculty of Health and Medical Sciences, Univ. of Surrey), Katharina, Nöh (Forschungszentrum Jülich GmbH)
 
12:10-14:10, Paper MoPP.16 Add to My Program
Identification of Patient Cystic Fibrosis Population Parameters Via Probabilistic and Profile Likelihood Estimates
Markovetz, Matthew (Univ. of Pittsburgh), Corcoran, Timothy (Univ. of Pittsburgh), Pilewski, Joseph (Univ. of Pittsburgh), Parker, Robert S. (Univ. of Pittsburgh)
 
12:10-14:10, Paper MoPP.17 Add to My Program
Workflow for Identification of Enzyme-Kinetic Networks
Spiess, Antje (TU Braunschweig)
 
12:10-14:10, Paper MoPP.18 Add to My Program
Using Rxncon to Model Signal Transduction at the Resolution of Empirical Data
Krantz, Marcus (Humboldt-Univ. Zu Berlin)
 
12:10-14:10, Paper MoPP.19 Add to My Program
Stochastic Multiscale Modeling of Influenza Virus Production in Cell Cultures
Rüdiger, Daniel (Max Planck Inst. for Dynamics of Complex Tech. Systems), Heldt, Stefan (Max Planck Inst. for Dynamics of Complex Tech. Systems), Reichl, Udo (Max Planck Inst. for Dynamics of Complex Tech)
 
12:10-14:10, Paper MoPP.20 Add to My Program
Integration of Single Cell and Population Data for Model Parametrization of the Yeast Cell Cycle
Schlichting, Julia Katharina (Humboldt-Univ. Zu Berlin), Amoussouvi, Aouefa (Humboldt Univ. Berlin), Schreiber, Gabriele (Humboldt Univ), Klipp, Edda (Humboldt-Univ. Zu Berlin)
 
12:10-14:10, Paper MoPP.21 Add to My Program
Modelling Carotene Desaturation Via Phytoene Desaturase (PDS)
Fehling-Kaschek, Mirjam (Univ. of Freiburg), Koschmieder, Julian (Univ. of Freiburg), Beyer, Peter (Univ. of Freiburg), Timmer, Jens (Albert-Ludwigs Univ. Freiburg)
 
12:10-14:10, Paper MoPP.22 Add to My Program
A Reaction-Diffusion Model to Describe Listeria Monocytogenes Biofilms Life Cycle
Balsa-Canto, Eva (CSIC), Vilas, Carlos (Inst. De Investigacions Marińas), Mosquera-Fernandez, Maruxa (IIM-CSIC), Briandet, Romain (INRA), Cabo, Marta L. (IIM-CSIC)
 
12:10-14:10, Paper MoPP.23 Add to My Program
Parameter Identification for Curli Fiber Expression Model
Kasielke, Stefanie (Zuse Insititute Berlin)
 
12:10-14:10, Paper MoPP.24 Add to My Program
Robustness and Filtering Properties of Ubiquitous Signaling Network Motifs
Paul, Debdas (Univ. of Stuttgart), Radde, Nicole (Univ. of Stuttgart, Inst. for Automatic Control)
 
12:10-14:10, Paper MoPP.25 Add to My Program
Zero-Retroactivity Subtraction Module for Embedded Feedback Control of Chemical Reaction Networks
Bilotta, Mariaconcetta (Univ. Degli Studi Magna Graecia Di Catanzaro), Cosentino, Carlo (Univ. Degli Studi Magna Graecia Di Catanzaro), Merola, Alessio (Univ. Degli Studi Magna Graecia Di Catanzaro), Bates, Declan G. (Univ. of Warwick), Amato, Francesco (Univ. Degli Studi Magna Graecia Di Catanzaro)
 
12:10-14:10, Paper MoPP.26 Add to My Program
Irreversible Port-Hamiltonian Approach to Modeling and Analyzing of Non-Isothermal Chemical Reaction Networks
Wang, Li (Univ. of Groningen), Maschke, Bernhard (Univ. De Lyon; Univ. Lyon 1,), van der Schaft, Arjan J. (Univ. of Groningen)
 
12:10-14:10, Paper MoPP.27 Add to My Program
Inferring the Effects of Positive and Negative Auto-Regulation under the Presence of Signalling Processes of Different Speed and Its Application to Inflammasome Signalling
Lopez-Caamal, Fernando (Univ. Nacional Autonoma De Mexico-UNAM), Huber, Heinrich (Royal Coll. of Surgeons in Ireland)
 
12:10-14:10, Paper MoPP.28 Add to My Program
Modulation of Noise in Regulatory Circuits for a Controlled Generation of Population Heterogeneity
Hahl, Sayuri Katharina (Tech. Univ. München), Kremling, Andreas (Tech. Univ. München)
 
12:10-14:10, Paper MoPP.29 Add to My Program
Stochastic Control with Poorly Known Biological Growth Models
Silva, Vinícius Lima (Univ. of Campinas), Do Val, Joao B.R. (Unicamp - Feec)
 
12:10-14:10, Paper MoPP.30 Add to My Program
Effective Detection of Multistationarity in Signaling Pathways with and without Mass Conservation
Otero-Muras, Irene (IIM-CSIC), Yordanov, Pencho (ETH Zurich), Stelling, Joerg (ETH Zurich)
 
12:10-14:10, Paper MoPP.31 Add to My Program
Unravelling the Mechanisms of Bistability in Flagellar Gene Regulation
Koriala, Santosh (Univ. of Illinois at Urbana-Champaign), Aldridge, Phillip (Newcastle Univ), Rao, Christopher V. (Univ. of Illinois)
 
12:10-14:10, Paper MoPP.32 Add to My Program
Iterative Multiple Linear Regression for Source Inversion in Graphs
Weber, Tobias (Otto Von Guericke Univ), Scholz, Eberhard (Univ. Hospital Heidelberg), Sager, Sebastian (Otto-Von-Guericke Univ. Magdeburg)
 
12:10-14:10, Paper MoPP.33 Add to My Program
The Impact of Experimental Data Quality on Computational Systems Biology and Engineering
Carius, Lisa (Otto Von Guericke Univ. Magdeburg), Findeisen, Rolf (Otto Von Guericke Univ. Magdeburg)
 
MoPAP Plenary Session, Nave Add to My Program 
Frank Doyle  
 
 
14:10-15:00, Paper MoPAP.1 Add to My Program
Systems Approaches to Treating Diabetes
Doyle, Francis (Harvard Univ)
 
MoKAP Keynote Session, Nave Add to My Program 
Rudi Gunawan  
 
 
15:10-15:40, Paper MoKAP.1 Add to My Program
Gene Regulatory Network Inference Using Time-Stamped Cross-Sectional Single Cell Expression Data
Papili Gao, Nan (ETH Zurich, Swiss Inst. of Bioinformatics), Ud-Dean, S. M. Minhaz (ETH Zurich, Swiss Inst. of Bioinformatics), Gunawan, Rudiyanto (ETH Zurich, Swiss Inst. of Bioinformatics)
 
MoCAP Coffee, Nave Add to My Program 
Coffee Break MA  
 
 
MoA1 Regular Session, Nave Add to My Program 
Modelling – Microbial Systems  
 
 
16:10-16:30, Paper MoA1.1 Add to My Program
In Silico Analysis of Clostridium Difficile Biofilm Metabolism and Treatment
Henson, Michael A. (Univ. of Massachusetts), Phalak, Poonam (Univ. of Massachusetts)
 
16:30-16:50, Paper MoA1.2 Add to My Program
Dynamic Macroscopic Model of Dengue Viral Amplification in Vero Cell Cultures
Abbate, Thomas (Univ. De Mons), Dewasme, Laurent (Univ. De Mons), Vande Wouwer, Alain (Univ. De Mons)
 
16:50-17:10, Paper MoA1.3 Add to My Program
Protein-Level Control of Metabolism: Design Principles and Prospects from a Representative System
Euler, Christian K. (Univ. of Toronto), Mahadevan, Radhakrishnan (Univ. of Toronto)
 
17:10-17:30, Paper MoA1.4 Add to My Program
A Fokker-Planck Equation Formalism to Model Bacterial Growth and Cell Size
García, Míriam R. (IIM-CSIC), Alonso, Antonio A. (IIM-CSIC), Teixeira, Isabel (Grupo De Oceanología (IIM-CSIC)), Vázquez, José Antonio (Grupo De Reciclado Y Valorización De Materiales Res. (REVA)
 
17:30-17:50, Paper MoA1.5 Add to My Program
A Collection of Mathematical Models Showing Diauxic Growth Behaviour
Kremling, Andreas (Tech. Univ. München)
 
MoA2 Regular Session, Gallery Add to My Program 
Methods  
 
 
16:10-16:30, Paper MoA2.1 Add to My Program
Structural Identifiability Analysis Via Extended Observability and Decomposition
Fernández Villaverde, Alejandro (Univ. De Vigo), Barreiro, Antonio (Univ. of Vigo), Papachristodoulou, Antonis (Univ. of Oxford)
 
16:30-16:50, Paper MoA2.2 Add to My Program
Identification of Functional Connections in Biological Neural Networks Using Dynamical Bayesian Networks
Dong, Chaoyi (Inner Mongolia Univ. of Tech), Yue, Hong (Univ. of Strathclyde)
 
16:50-17:10, Paper MoA2.3 Add to My Program
Reconstruction of Ensemble of Single-Cell Time Trajectories from Discrete-Time Fluorescence Data: Oscillatory MAPK Dynamics
Kalantre, Girija S. (Indian Inst. of Tech. Bombay), Viswanathan, Ganesh A. (Indian Inst. of Tech. Bombay)
 
17:10-17:30, Paper MoA2.4 Add to My Program
Analysis of Circadian Cellular Bioluminescence Recordings Using a Kalman Smoother
Ananthasubramaniam, Bharath (Charite Univ)
 
17:30-17:50, Paper MoA2.5 Add to My Program
Efficient Computation of All Distinct Realization Structures of Kinetic Systems
Tuza, Zoltan A. (Univ. of Stuttgart), Acs, Bernadett (Pazmany Peter Catholic Univ), Szederkenyi, Gabor (Computer and Automation Res. Inst. Hungarian), Allgöwer, Frank (Univ. of Stuttgart)

 
 

 
 

 

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